kinome: Example Data from InfectX

In pmm: Parallel Mixed Model

Description

Data from gene knock-down experiments performed with 11 siRNA for 8 different pathogens. The data was generated by the InfectX consortium.

Usage

data(kinome)

Format

The data frame contains the microscope image readouts of 826 kinases knock-down experiments. For each gene cells were targeted by a total of 12 independent siRNAs coming from three manufactures: Ambion (3 siRNAs), Qiagen (4 siRNAs) and Dharmacon (4 siRNAs + 1 pool siRNA). All experiments were conducted for 8 different pathogens. Each row of the data frame corresponds to the result of one experiment.

GeneID	ID of the gene that is knocked down.
GeneName	Name of the gene that is knocked down.
company	Company that provided the siRNA for knock-down.
siRNA	Label to identify the different siRNA replicates that are used.
CellCount	normalized image readout describing the number of cells in the well
InfectionIndex	normalized image readout describing the number of infected cells in the well
weight_library	weight denoting the quality of libraries. We assigned a higher weight to
	Dharmacon Pooled and Ambion libraries (weight 2) than to the unpooled
	libraries Dharmacon and Qiagen (weight 1).

Value

data.frame

Note

All of our screening data, including raw images, are available at the openBIS portal (http://infectx.ch/dataaccess).

References

Rämö, P., Drewek, A., Arrieumerlou, C., Beerenwinkel, N., Ben-Tekaya H., Cardel, B., Casanova, A., Conde-Alvarez. R., Cossart, P., Csucs, G., Eicher, S., Emmenlauer, M. Greber, U., Hardt, W.-D., Helenius, A., Kasper, C., Kaufmann, A., Kreibich, S., Kuebacher, A., Kunszt, P., Low, S.H., Mercer, J., Mudrak, D., Muntwiler, S., Pelkmans, L., Pizarro-Cerda, J., Podvinec, M., Pujadas, E., Rinn, B., Rouilly, V., Schmich F., Siebourg, J., Snijder, B., Stebler, M., Studer, G., Szczurek, E., Truttmann, M., von Mering, C., Vonderheit, A., Yakimovich, A., Buehlmann, P. and Dehio, C., Simultaneous analysis of large-scale RNAi screens for pathogen entry, BMC Genomics 15(1162): p.1471-2164. (2014)

Examples

data(kinome)
str(kinome)
head(kinome)

pmm documentation built on Nov. 8, 2020, 6:55 p.m.